[BioC] problem in diagnostic plots?

Robert Gentleman rgentlem@jimmy.harvard.edu
Wed, 31 Jul 2002 10:57:15 -0400


On Wed, Jul 31, 2002 at 07:19:10PM +1000, Peter Baker (CMIS, Indooroopilly) wrote:
> Hi All
> 
> I've just started using Bioconductor and seems really good.
> 
> As a test, I've read in two GenePix files - essentially the same code
> as ReadSpot example and seem to be able to plot, print, normalise ....
> 
> The only problem I've encountered is
> 
> > maDiagnPlots1(test[,2])
> Error in plot.new() : Figure margins too large
> > maRawPlots(test[,2])
> Error in plot.new() : Figure margins too large
> > maNormPlots(test[,2])
> Error in maMloc(structure(list(), maRf = structure(c(4109, 771, 3073,  : 
> 	No direct or inherited method for function "maMloc" for this call
> 

 Hi,
  We have had at least one similar report. I am not sure what the
  problem is precisely. Perhaps the names for the axis labels or some
  text is too long. We will have a look and see if we can sort out
  what the problem is.

   Robert

> I get the first plot only - seems to stop at the second
> 
> Does anyone recognise this sort of problem?
> 
> Could it be missing values? Do I need to filter these in some way
> before plotting? The arrays have row 10 of each 'block' empty
> 
> ------------------------------------------------
> 
> However, plots like these work absolutely fine
> 
> ### backgrounds
> maImage(test[,1], x = "maGb", contour=TRUE)
> maImage(test[,1], x = "maRb", contour=TRUE)
> 
> ### raw images
> maImage(test[,1])
> 
> > version
>          _                
> platform i686-pc-linux-gnu
> arch     i686             
> os       linux-gnu        
> system   i686, linux-gnu  
> status                    
> major    1                
> minor    5.1              
> year     2002             
> month    06               
> day      17               
> language R                
> 
> > Sys.info()
>      sysname                               release 
>      "Linux"                         "2.4.18-5smp" 
> (RedHat linux 7.3)
> 
> Thanks for your help
> 
> Regards
> Peter
> 
> 
> -- 
> Dr Peter Baker, Statistician (Bioinformatics/Genetics),
> CSIRO Mathematical & Information Sciences,
> 120 Meiers Rd, INDOOROOPILLY, QLD 4068.  Australia. 
> Email: <Peter.Baker@csiro.au>
> WWW: http://www.cmis.csiro.au/Peter.Baker/
> Phone:+61 7 3214 2210   Fax:+61 7 3214 2881
> 
> 
> 
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-- 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20
| Harvard School of Public Health  email: rgentlem@jimmy.dfci.harvard.edu   |
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